From my very limited experience, organic matter generally settles considerably faster than clay. Placing aggregate over the clay will help keep it from being disturbed and disolved into the water. You're going to have the organic matter either way. Rather than a waterproof pond liner you may consider contacting a geotextile fabric manufacturer for a more cost effective alternative. The fabric will help keep whatever aggregate you choose from sinking into the underlying clay but will not have any water retaining value. I agree with everything Mr. Cody has said and organics will settle in over time. Aeration and active weed prevention will reduce the amount of build up you get. It seems that if aeration was properly placed it could help keep an area somewhat clear of settling debris, think about a slack water area of a creek where leaves and sticks settle vs. the clear moving water section.



"The greatest enemy of knowledge is not ignorance, it is the illusion of knowledge." Stephen W. Hawking